During Avengers: Age of Ultron, after Scarlet Witch messed everyone and they ended up at Hawkeye's place, Thor took off to find some answers for what he saw. He ended up contacting the scientist played by Stellen Skarsgard. They ended up at some pool of water where Thor goes all lightning and stuff, but I didn't really follow what was happening.

So, what was Thor doing? Why did he do this and what were the results?

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The visions that Scarlet Witch gave to the various Avengers basically played on their worst fears, e.g. Tony saw the Avengers dead because he failed; Natasha relived her training in the Red Room, etc.

For some reason (that I don't think is adequately explained in the movie), Thor's vision was far more directly relevant than the others. As an Asgardian, Thor is likely far more aware of the kind of dangers that exist in the broader universe, and he's also aware of the fact that at least two of the Infinity Stones have been put in play recently. Those things would be his "worst fears" -- something so dangerous that it could literally destroy the entire universe.

In his vision, he sees flashes of those stones (including the Mind Stone), but doesn't immediately understand what it means, so he goes off to find answer. The place that he travels, to get those answers, is named "The Water of Sight" by Dr. Selvig. Again, we don't know much about them except what Thor and Selvig say about them in that one scene, but they are apparently a magical spring that allows Thor to access information he would not normally have.

As Thor indicates, if the Waters "accept" him, they will grant him much better understanding of his vision and what it means. The knowledge he gains from the Waters lead him to understand that the Mind Stone is in play, and that he needs to ensure that Vision is allowed to exist and keep control of the Stone.

This eventually leads him to go back to Stark Tower and help Tony create Vision.